Ncbi-fcs: Difference between revisions
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Created page with "Category:SoftwareCategory:BiologyCategory:Genomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|ncbi-fcs}}https://github.com/ncbi/fcs |{{#vardefine:url|}} <!..." |
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[[Category:Software]][[Category:Biology]][[Category:Genomics]] | [[Category:Software]][[Category:Biology]][[Category:Genomics]] | ||
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|ncbi-fcs}}https://github.com/ncbi/fcs | |{{#vardefine:app|ncbi-fcs}} | ||
|{{#vardefine:url|https://github.com/ncbi/fcs}} | |||
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
|{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> | ||
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
| Line 26: | Line 26: | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
* GXDB_LOC - database directory | |||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
* unset PYTHONHOME after loading the ncbi-fcs module | |||
* request at least 512 GiB memory to hold the database and accessory files. | |||
* copy the full "gxdb" database to the slurm $TMPDIR | |||
* set $GXDB_LOC environmental variable to point to $TMPDIR | |||
cp -r "$GXDB_LOC/gxdb" $TMPDIR/gxdb | |||
export GXDB_LOC=$TMPDIR | |||
|}} | |}} | ||
Latest revision as of 19:25, 28 February 2025
Description
Foreign Contamination Screening caller scripts and documentation.
Environment Modules
Run module spider ncbi-fcs to find out what environment modules are available for this application.
System Variables
- HPC_NCBI-FCS_DIR - installation directory
- HPC_NCBI-FCS_BIN - executable directory
- GXDB_LOC - database directory
Additional Information
- unset PYTHONHOME after loading the ncbi-fcs module
- request at least 512 GiB memory to hold the database and accessory files.
- copy the full "gxdb" database to the slurm $TMPDIR
- set $GXDB_LOC environmental variable to point to $TMPDIR
cp -r "$GXDB_LOC/gxdb" $TMPDIR/gxdb export GXDB_LOC=$TMPDIR